9-94456060-C-T

Variant names:

• chr9-94456060-C-T
• rs2277182
• NM_032558.3:c.1029-180C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032558.3(SLC71A2):​c.1029-180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,830 control chromosomes in the GnomAD database, including 19,775 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19775 hom., cov: 31)
• Consequence: SLC71A2 NM_032558.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 11 publications found

Genes affected

SLC71A2 (HGNC:23376): (major facilitator superfamily domain containing 14B) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC71A2	NM_032558.3	c.1029-180C>T		intron_variant	Intron 9 of 11	ENST00000375344.8	NP_115947.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD14B	ENST00000375344.8	c.1029-180C>T		intron_variant	Intron 9 of 11	1	NM_032558.3	ENSP00000364493.3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77006 AN: 151710 Hom.: 19747 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.513

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.508 AC: 77089 AN: 151830 Hom.: 19775 Cov.: 31 AF XY: 0.514 AC XY: 38116 AN XY: 74180

African (AFR) AF: 0.535 AC: 22144 AN: 41352

American (AMR) AF: 0.603 AC: 9211 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1915 AN: 3464

East Asian (EAS) AF: 0.401 AC: 2071 AN: 5166

South Asian (SAS) AF: 0.507 AC: 2431 AN: 4798

European-Finnish (FIN) AF: 0.515 AC: 5418 AN: 10526

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32166 AN: 67940

Other (OTH) AF: 0.509 AC: 1073 AN: 2106

Alfa AF: 0.463 Hom.: 8087

Bravo AF: 0.518

Asia WGS AF: 0.482 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.23
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2277182; hg19: chr9-97218342;